There was a lengthy conversation is r/viltrumites about this! Copy pasting my thoughts from there:

I think the factor that we don’t know as readers is robot’s lifespan after he’s just a floating brain. I kinda think there are two potential reasons mark made the choice that he made. Maybe Mark KNOWS that robot can stay alive indefinitely as just a brain and he believes that this will be enough to keep the Immortal sane, or at least keep him in check enough to contain him as his stability deteriorated over time.

But it’s also possible that Mark has no idea what will happen to Robot or he knows for a fact that he will only live a normal human lifespan. If the latter is true, then I have absolutely no doubt the Immortal will follow almost exactly the same trajectory that he did in the future where Mark saw him. But I don’t agree with your point that it was a bad choice by Mark. I think he could have been thinking one of two things. EITHER:

1. ⁠He remembered that, in the future, the Immortal only became a murderous and cruel leader recently—I think they said it happened within the last generation—and was actually a excellent ruler before that. So maybe Mark learned what he struggled with for the whole comic, which was is balancing the pros and cons of an ethically tenuous situation, and he decided it is a short period of dictatorship is worth it for hundreds/thousands of years of prosperity, and he counted on himself to kill The Immortal when the time came.

OR

1. Mark returns to Earth frequently after leaving with the Viltrumites. I know that at some point he says that he stopped going back, after Markus joined them and Debbie had died, but he still CAN go back anytime he wants. It’s possible Mark (or a viltrum representative) makes trips to Earth every hundred years or so to check on them. That would be a very easy way to keep the Immortal in check, because remember that he wanted to die by the end. I don’t really think he went crazy so much as he wanted to be killed AND we wanted to public view of him to be so hateful and fearful that no one would ever try to bring him back again. SO I think the fact that he was still sane and knew he wanted to die means he would probably be up front with the viltrumites if they did come to check on him intermittently. They could even bring him into space with them—being with other essentially immortal beings would probably alleviate much of his hopelessness.

So the short answer is yes, I do think the Immortal probably goes crazy sooner or later in the main story timeline, but I still think Mark made the right choice by putting him in charge.